Feeling the shapes of molecules

The atomic structure of a small organic molecule can be revealed by atomic force microscopy.

Philip Ball

Scientists have worked out the correct chemical structure of cephalandole A (left) by using an atomic-force microscope to map its atoms (middle) and its electron density (right).Gross, L. et al

The atomic-scale architecture of a complicated small molecule has been deduced by scanning and 'feeling' it, using a technique called atomic force microscopy.

Reporting their work in Nature Chemistry1, researchers have been able to distinguish between two possible molecular structures of a substance from a deep-sea bacterium by using a very fine needle-like tip to trace out the shape of the molecule lying on a crystal of salt.

Determining the way that atoms are connected together in a molecule has previously relied on indirect methods, such as reflecting X-rays off crystals of the material (X-ray crystallography) or looking at how the atoms of the molecule absorb radio waves (nuclear magnetic resonance or NMR).

In contrast, Leo Gross of IBM's research centre in Zurich, Switzerland, and his co-workers have used two types of scanning probe microscopy to take snapshots of a molecule's shape directly.

"It's certainly an interesting result, and another possible tool in the toolbox for determining structure," says Judith Howard of Durham University, UK, a specialist in the X-ray crystallography of small organic molecules. X-ray crystallography can reveal a molecule's three-dimensional (3D) atomic structure — but only if good-quality crystals of the substance can be grown. This is sometimes not possible either because too little of it is available or because the compound does not crystallize.

The scanning tunnelling microscope (STM), devised at IBM Zurich in the 1980s, can reveal the structures of molecules and materials with atomic precision by measuring the electrical current that flows between a moving electrically charged metal tip and the sample positioned just beneath it. This current depends on both the chemical nature of the sample and how close it is to the tip.

The closely related atomic-force microscope (AFM) 'feels' a sample's atomic-scale structure directly by measuring the attractive force between it and the tip, which depends on the distance between them.

Bright blobs

Although both the STM and AFM can in principle show individual atoms on a flat surface, molecules tend to show up as bright blobs with the atoms merged together. And the shape of the blob only reflects the shape of the whole molecule if it is lying flat on the surface.

Last year, Gross and his colleagues showed for the first time that, by using scanning tips topped with a single molecule of carbon monoxide (CO), they could make an AFM sensitive enough to trace out the atomic framework of a small organic (carbon-based) molecule on a surface2. But in that case, they were able to compare their images with those predicted from the already-known structure of the molecule.

In the new work, they were aiming to distinguish between two or more possible molecular structures in a case where the standard techniques had not been able to decide between them. This would test whether the AFM could not just confirm what we know but clarify what we do not.

Gross and colleagues chose to study a molecule made by bacteria that live under high pressure in the deepest part of the oceans, 11 kilometres below the surface. Called cephalandole A, it is one of many such 'natural products' being investigated for possible use as a drug.

The atomic structure of cephalandole A had previously been deduced using NMR, which reveals the relative positions of pairs of atoms. That method suggested four possible structures, but could not easily distinguish them: although one was preferred initially, another was later identified as a better candidate, showing how ambiguous the NMR experiment was.

Snapshot view

The team's STM and AFM images of a cephalandole A molecule lying on a salt crystal clearly showed the molecule's general shape, with some of the hexagonal rings of atoms that it was known to contain being visible.

But by themselves, these images were not detailed enough to decide which of the two best structures suggested by NMR was the right one. However, the researchers could also calculate what the AFM images should look like for each structure, and found that only one of them closely fitted the images obtained.

It remains to be seen how generally useful the method will be. Christian Joachim, an STM specialist at the Centre for Materials Elaboration and Structural Studies in Toulouse, France, cautions that "many researchers are still debating what these AFM images with a CO tip are really showing". Also, he worries that the structure of a molecule might be altered when it is deposited on a crystal surface. "The technique often used for deposition is very destructive", he says.

Howard agrees that the structure of the molecule in such conditions might not be representative. "Any perturbation in shape must be allowed for, and this can only be done when you are fairly confident about the overall shape to start with", she says.

"It's not going to replace crystallography as the gold standard", Howard concludes. "We can solve structures using crystallography without any prior information, but as yet I don't think this method does or can."